1 About the analysis

The plots here come from an analysis from Kalucka supplementary data, where the different markers posted have been taken and analysed over the 20-01-2021 Liver scRNASeq experiment. In said experiments there are four different set of Conditions, Control, Dll4KO, RbpjKO and Notch1KO. In said experiment it has been observed that the traditional arterial phenotype is lost in LOF mice, yet mice can still function. Therefore, we hipothesise that Endothelial Cells develop a new kind of arterial phenotype as an emergency mechanism due to lack of proper traditional arterial EC differentiation.

For this reason we set into looking at different markers that have been validated as arterial, venous or capillary phenotypes and look at the spread in the 20-01-21 Liver experiment, with the aim of finding a considerable difference in the spread between the Control and the 3 LOF samples. Ideally we want to localize the cluster where the arterial “emergency” phenotype forms in the LOF samples.

2 About Kalucka marker setup

The Kalucka supplementary data separates the data in different set of categories, them being:

  1. Top 50 highly expressed genes in their own selected clusters: 1a. Large artery 1b. arterial capillary 1c. capillary 1d. venous capillary 1e. venous
  2. Conserved markers across tissues 2a. artery 2b. vein 2c. capillary
  3. Specific markers in each tissue (liver) 3a. artery 3b. vein 3c. capillary
  4. Proliferating
  5. Metabolic

The same criteria will be used when showing the plots.

3 Objective

We want to see a clear difference in the arterio-venous differentiation spread of Control vs. LOF (Dll4, Rbpj, Notch1) samples

4 Analysis

library("Seurat")
library("openxlsx")
library("knitr")
library("rmarkdown")
library("yaml")
Carlos <- readRDS("SC.Analysis.SecondPass.RNA.Singlets.Endothelial.ManualClustering.seuratSC.Final.V4.rds")

4.1 1.Top 50 highly expressed genes in their own selected clusters

4.1.1 a. Large Artery

Top50_large_artery Top50_large_artery_Vln

4.1.2 b. Arterial capillary

Top50_arterial_capillary

Top50_arterial_capillary_Vln

4.1.3 c. Capillary

Top50_capillary Top50_capillary_Vln

4.1.4 d. Venous Capillary

Top50_capillary_venous Top50_capillary_venous

4.1.5 e. Venous

Top50_venous Top50_venous_Vln

4.2 2.Conserved markers across tissues

4.2.1 a. Artery

Conserved_artery

4.2.2 b. Vein

Conserved_vein

4.2.3 c. Capillary

There were no remarkable markers in this section (capillary markers tend to be expressed in all cells)

4.3 3. Specific markers in each tissue (liver)

4.3.1 a. Artery

Specific_Artery

4.3.2 b. Vein

Specific_Vein

4.3.3 c. Capillary

Again, no remarkable markers to be found here

4.4 4. Proliferating

Proliferating Proliferating_Vln

4.5 5. Metabolic

Metabolic Metabolic_Vln

4.6 6. EDNRB

EDNRB <- FeaturePlot(Carlos, split.by = "Condition", features = "EDNRB")
EDNRB

EDNRB EDNRB

EDNRB